ArticleNucleic acids research2018
Assessing genome assembly quality using the LTR Assembly Index (LAI).
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 614 papers.
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614 citing papers in PubMed.
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- The heterozygous pineapple genome demonstrates the importance of haplotype-resolved plant genomes.Horticulture research · 2026Article
- Near telomere-to-telomere genome assembly enables the discovery of introgressed purple-leaf geneHorticulture research · 2026Article
- Contrasting regulation of protein-coding genes and lncRNA homeologs in allotetraploid Coffea arabica.Planta · 2026Article
- Chromosome-scale genomes and population resequencing resolve subgenome diversity and halophyte adaptation in Salicornia.Nature communications · 2026Article
- Chromosome-scale assembly of wheat cultivar Sumai 3, a major germplasm source for Fusarium head blight resistance.The plant genome · 2026Article
- A pangenome-based approach reveals genes associated with polyploidy and apomixis in Eragrostis curvula.The plant genome · 2026Article
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- First chromosome scale genome of Acrocomia aculeata.Scientific data · 2026Article
- Phased-genome assemblies of saltgrass reveal structural dynamics and genomic basis for extreme salt tolerance and dioecy.Plant communications · 2026Article
- Genomic basis of scent loss and functional divergence in wild and cultivated carnations (Horticulture research · 2026Article
- Genome assembly of Astatotilapia latifasciata uncovers B chromosome-linked chromatin reorganization.Heredity · 2026Article
- The telomere-to-telomere genome and comparative analysis from algae to higher plants reveal origin and evolution of biosynthesis of chlorogenic acid pathway and production in ramie (Horticulture research · 2026Article
- Chromosome-scale assembly of the eliteHorticulture research · 2026Article
- De novo haplotype-resolved genome assembly of the endemic kiwifruit Actinidia hubeiensis.Scientific data · 2026Article
- East-west divergence and metabolic differentiation in celery domestication.Nature communications · 2026Article
554 more citing papers are in PubMed but not listed here.
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Assembling a plant genome is challenging due to the abundance of repetitive sequences, yet no standard is available to evaluate the assembly of repeat space. LTR retrotransposons (LTR-RTs) are the predominant interspersed repeat that is poorly assembled in draft genomes. Here, we propose a reference-free genome metric called LTR Assembly Index (LAI) that evaluates assembly continuity using LTR-RTs. After correcting for LTR-RT amplification dynamics, we show that LAI is independent of genome size, genomic LTR-RT content, and gene space evaluation metrics (i.e., BUSCO and CEGMA). By comparing genomic sequences produced by various sequencing techniques, we reveal the significant gain of assembly continuity by using long-read-based techniques over short-read-based methods. Moreover, LAI can facilitate iterative assembly improvement with assembler selection and identify low-quality genomic regions. To apply LAI, intact LTR-RTs and total LTR-RTs should contribute at least 0.1% and 5% to the genome size, respectively. The LAI program is freely available on GitHub: https://github.com/oushujun/LTR_retriever.
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